MERMAID is an open-source application that collects and manages real-time coral reef health data, developed in partnership between the WCS, WWF, and Sparkgeo.

With MERMAID, scientists input their observations straight into the platform using the Web app. MERMAID does the job of tagging and sorting data, avoiding duplicates, standardizing scientific names and summarizing critical indicators.

We save you time so you can save coral reefs!

MERMAID joins you in the field with its off-line capabilities, but it stands apart from Excel or personal database apps like Access because it requires virtually zero post-entry data clean up! 

Users can select reef fish and coral names from a standard list of taxa with only a few keystrokes; MERMAID will autocomplete the rest. Selecting names means saving time typing in species names or cleaning up typos of misspelled species names.

MERMAID also allows you to calculate reef fish biomass while you type, or see your total coral cover as soon as you have finished entering a transect. When you have finished collecting data, it can be exported to standard field reports (Excel) and used to create graphs or other reports. You can also analyze your data by accessing it directly from MERMAID using the mermaidr package.

The MERMAID workflow:

1. Sign up and set up a project

   1. Sign up for an account

   2. Set up a project and add users

   3. Prepare for off-line use

2. Collect data

   1. Select a transect type

   2. Enter site information

   3. Enter management regime

   4. Include benthic attributes and fish species

   5. Complete and save the transect

3. Review and submit 

   1. Validate data

   2. Address errors and warnings

   3. Submit data

4. Export and analyze data

   1. Export to .XLSX for further analysis

   2. Analyze directly using mermaidr

Questions? You can reach out to us when online via the Contact link at the bottom of the app. An off-line (pdf) version of this documentation is available through the "Download" button at the left menu bar.

The Projects Page

The Projects Page provides a complete summary of what is happening in each project: the number of submitted and unsubmitted sample units, the total number of sites with data, the number of users added to the project, and how the per-protocol data sharing policies have been set. Click on each to go directly to the specific project page; for example, you can access a project's Submitted data page by clicking Submitted. MERMAID Version 2 also added an all-new notification area in the menu (the "bell") that informs you of the latest updates from MERMAID and your projects. Close to the notification button, you can find the Reference button which you can access from any page. Now, you can download References in XLSX format and have all the benthic and fish data in one document. Each project also includes the Copy project and Off-line Ready buttons from MERMAID Version 1.

The Overview Page

As a data manager, you might want to see at a glance all the data that has been submitted as well as who to chase for unsubmitted data. MERMAID Version 2 understands you. It now has Overview pages that allow you to inspect the number of submitted sample units per method for each site as well as who has not yet submitted which sample units, and make sure that sites are associated with the right management regimes. Clicking on any sample unit number provides you with direct access to that sample unit. To make changes, the sample unit must be moved from the Submitted to the Collecting page. Re-validation is required before submitting the updated sample unit. This means no more unexpected site changes or other unintended errors.

The Collecting Page

The new Collecting Page is designed to allow users to handle warnings and errors more easily. It also shows a reminder of why a sample unit cannot be submitted, to help you address problems more quickly. Messages are easier to read and appear next to the field where the problem is. MERMAID Version 2 also deals with site and management regime duplications in a smarter way; Version 1 would check for duplication every time a site or management regime was saved, whereas in Version 2, duplication is checked only with sample unit validation, and only against submitted sample units -- a more efficient and more relevant process. The photo transect method is now available in MERMAID Version 2 to store your photo classification results. On the Submitted page, the Export to XSLX button now produces a single file with data aggregated to sample unit and sample event levels as well as raw observations.

The Users Page

The new Users page provides more detailed information on users in the project, for teams of any size. MERMAID Version 2 supports filtering users by name or email address. Admins can also change roles, add and remove users without going to another page, and access the user's email addresses for easy contact.

See our MERMAID Version 2 announcement. If you have any questions or want to learn more about MERMAID Version 2, contact us.

Click on 'Reference' in the main toolbar (upper right of the MERMAID Collect app) to download an xlsx file of all benthic attributes and fish species / genera / families that are used in MERMAID. This works offline as well as online.

In the xlsx file, you will find five sheets: Fish Families, Fish Genera, Fish Species, Fish Groupings, and Benthic. Each sheet provides information for that taxonomic level. Using filters, you can search and sort for the specific information you are looking for.

Fish and benthic attributes in MERMAID are standardized, and aligned with accepted names in the World Register of Marine Species (WORMS), eliminating discrepancies between different users' data. However, if you want to record an observation of something you think is missing, you can propose to add it in the app, and it will be reviewed by the MERMAID team. Before adding a new fish or benthic species, please make sure that you are using the accepted scientific name by WORMS.

Once you propose a new fish species or benthic attribute, you can directly use it while entering data. The MERMAID team will either accept your proposal, making it available for all other MERMAID users, or work with you to normalize the proposed species or attribute with an existing one; either way, we will let you know by email.

Propose new fish species

1. In any fish belt transect, scroll down to the Observations table.
2. Type the fish species that you want to add. When what you have typed does not match any fish species in MERMAID, the option to propose a new species will appear.
3. Click the “Propose New Species” option.
4. Type the genus name in the Genus field. If the genus you are looking for is not there ("No results found"), send us an email by clicking “Contact” button in the bottom right of the app.
5. Type the species name in the Species field and click "Next".
6. Click "Send to MERMAID for review" to complete your proposal.

Propose a new benthic attribute

1. In any benthic transect, scroll down to the Observations table
2. Type the benthic attribute that you want to add. When what you have typed does not match any benthic attribute in our database, the option to propose a new benthic attribute will appear.
3. Click the “Propose New Benthic Attribute” option.
4. Type the parent name in the Parent field. Typically, "Parent" will be a coral genus or family, but can be a non-trophic attribute. For example, to add a new Acropora species named Acropora test, type/select Acropora in the Parent field, then type Acropora test in the Name field, and click “Next”.
5. Click "Send to MERMAID for review" to complete your proposal.

Standard taxonomic hierarchies

MERMAID has developed a single set of standard taxonomic hierarchies for reef fish and benthic observations that are shared across the MERMAID Collect, Dashboard and R Package apps. This eliminates lengthy data cleaning, simplifies analysis, and makes it easy to create reproducible charts and reports from your data. 

Reef fish observations aggregate from species to genus to family to trophic group (e.g. herbivore, planktivore, etc). 

Benthic observations aggregate from species to genera to family to a benthic top-level category (e.g. hard coral, soft coral, macroalgae).

Reef fish observations 

For reef fish observations, the biomass constants, maximum length, trophic level, fishing vulnerability, climate score, and geographic distribution are drawn from FishBase. 

• Since reference values of biomass constants and trophic level are provided by species in FishBase, when using a genus- or family-level fish observation in Collect, MERMAID automatically averages species-level values. For example, typing "Acanth'' allows you to record an observation for the "Acanthuridae" family, the "Acanthurus" genus, or the "Acanthurus achilles" species; if you chooose "Acanthurus" biomass constants will be the averages of all species in the "Acanthurus" genus.

Benthic observations 

MERMAID uses a hierarchical taxonomy of benthic attributes. This means that every attribute can be ‘rolled up’ into one of 12 top-level benthic categories which are available in xlsx data downloads from MERMAID and shown in the MERMAID dashboard.

The 12 top-level categories are:

• Bare substrate (e.g., rock)
• Crustose coralline algae
• Cyanobacteria
• Hard coral
• Macroalgae
• Other (e.g., trash, plastic, etc)
• Other invertebrates
• Rubble
• Sand (including silt)
• Seagrass
• Soft coral
• Turf algae (including dead coral or dead coral with algae)

For example, ‘Acropora palmata’ rolls up to ‘Acropora’ then ‘Acroporidae’ then the final top-level category of ‘Hard coral’. Top-level category classifications are provided as a separate column in xlsx downloads from your submitted MERMAID data. 

• Custom analyses, such as calculating percentages for benthic attributes that are not top-level categories, can be done using observation-level data by exporting submitted data from a project or accessing directly using the mermaidr package.

Using a ‘blank’ filter in the Parent column of the Reference xlsx file will provide you with a list of the 12 top-level categories.

Filtering for a specific benthic attribute in the "Parent" column will show all benthic attributes that belong to it.

After your data has been saved, it can be validated. Validation is the “proofreading” of the sample unit information and observations. This is where mistakes and outliers are caught and brought to your attention to correct. Site and management regime validations are checked only against submitted sample units. A reminder of why a sample unit cannot be submitted is shown under the Submit button to help you address problems more quickly.

Validation can only be done online.

After saving a transect, click the activated red “Validate” button to validate your transect.

After successfully validating a transect and resolving any errors or warnings, the Validate button will be grayed out and the Submit button will be activated in red.

After validating, you will receive one of the following results:

A. Success!

Nice work, your sample unit was validated successfully! There are no errors with the data and it is ready to submit.

B. Warnings

A yellow warning will appear at the top of the page or by and individual form field if MERMAID identifies a potential issue in your transect information. Warnings are validations that identify entered data that are possible, but unusual.

You can decide whether each warning can safely be ignored for your data. If the issue resulted from a data entry mistake, you can correct the data in the field, or in some cases by clicking a “Resolve” button to open a dialog where you can add or change the information. Click “update” to incorporate your changes into the transect. You can also navigate to fields with issues by clicking 'Scroll to observations' next to the warning.

After addressing warnings, resave the transect and validate again. Repeat the process for any additional warnings that are identified. If you don’t believe a warning is accurate for your transect, you can disregard it by clicking the 'Ignore warning' checkbox next to the warning.

C. Errors

A red warning message will appear if MERMAID identifies an error in a sample unit’s information or observations. Errors must be resolved before a transect can be submitted; they cannot be ignored. To address each error, scroll down to the field that has the 'ERROR' notice and directly change the information.

After resolving all errors, resave the transect and validate again. Repeat the process for any additional errors that are identified, until all 'ERROR' notices have disappeared.

D. Submit data

When you are finished entering data for a sample unit and have resolved all Errors and Warnings, you can Submit the sample unit.

After submitting data, admin users can still edit the transect or return a transect to the observer, so as a collector, make sure your data are finalized and clean before submitting! Submitting data can only be done when online.

To submit data, select the red button in a validated transect that says “Submit”.

Submitting data moves it from the "Collecting" page to the "Submitted" page. This shares your observations with the other users in the project (and depending on Data Sharing settings, potentially with the world). Within the “Submitted” page, admins can edit or delete transects or return them to their original observers for further editing.

If you are a read-only member on a project you can see data once it has been submitted and you can export it, but you cannot edit this data while it is in MERMAID.

You can also view your submitted data per project in the MERMAID Dashboard directly from the Collect app. Simply click on the icon 'View on Dashboard' next to the project name to navigate to the dashboard.

The OVERVIEW area provides project-level views of how a project is progressing and easy ways to find out who to chase for missing data. It is also enchanced with filtering by method feature through a butten next to the search bar. This feature allows users to filter in multiple ways. The total sample unit using the chosen method(s) will appear next to the filter button.

The 'Observers and Transects' page summarizes the number of submitted and unsubmitted transect(s) per site and method. Hover over each transect number to see detailed information including who was the last person editing the transect, who were the observer(s) collecting the transect, site name, management regime, and collecting date. You can also head to the submitted transect by clicking the 'View Submitted Sample Unit'.

The 'Management Regimes Overview' summarizes the number of submitted (not unsubmitted) sample units per management regime. Management regimes that have no submitted transects will not appear in the 'Management Regimes Overview' table. You can click on the transect number to jump to the submitted sample unit information.

If you are new to MERMAID and have existing data from past surveys in other formats that you would like to add to MERMAID, you can use our R package mermaidr to upload this old data into MERMAID. 

The workflow for uploading data should only be used for existing 'legacy' data. For an ongoing project, it is easier and better to enter your underwater observations directly in the app.

Steps for ingestion using the mermaidr package:

1. Create a project in MERMAID with sites, management regimes, and users added.

2. Adjust your data format to the MERMAID template. You can download the template for each method using the mermaid_import_get_template_and_options function from the MERMAID R package mermaidr. More information on how to use it can be seen here.

3. Ensure the mandatory fields are filled. Mandatory fields include an asterisk (*) sign in the column name. Download our example of PIT data using the MERMAID template here.

4. Check each field to make sure it matches allowed field options for importing data for a given method. To check each field, use the mermaid_import_check_options function from the MERMAID R package mermaidr. More information and example on how to use it can be seen here. A field that matches will produce a green check sign.

5. After all fields have passed the checking process, you can import your data using the mermaid_import_project_data function from the MERMAID R package mermaidr. Detailed information and an example can be seen here.

All ingested data will appear on the Collecting page. These data will need to go through the regular validation and submission process. For an example how to ingest your legacy data using the MERMAID R package mermaidr, head to the ingesting fishbelt data example.

Unsubmitted ingested transects appear on the Collecting page of the user who did the ingesting. To transfer unsubmitted sample units to another user, a project admin can use the project's Users page.

Read and download here the step-by-step guide on how to upload your existing data into MERMAID using the mermaidr package in R.

Try Easy PQT

Photo benthic quadrat data that are annotated using CoralNet can be imported to MERMAID in two ways, i.e., the MERMAID R package mermaidr and Easy PQT. Using the MERMAID R package mermaidr to upload your photo benthic quadrat data to MERMAID requires a good knowledge of R. If you are familiar with R, you can follow the steps in the Upload spreadsheets documentation, which has all the information you need, including the tutorial video and examples.

Another way to upload your photo benthic quadrat data is using the Easy PQT app. Easy PQT is a shiny app that supports MERMAID users, especially users unfamiliar with R, who want to upload their CoralNet exported data to MERMAID. It’s straightforward and user-friendly. Similar to using the MERMAID R package mermaidr, your data will appear on your Collecting Page after you upload it using Easy PQT. However, you will need to fill in some of the mandatory fields on MERMAID before validating and submitting your data. See the Easy PQT workflow below:

Only an admin of a project can upload data using Easy PQT and make sure that your project is not a test project. A test project will not appear on the Easy PQT list of projects.

Steps to upload your CoralNet exported data using Easy PQT:

• Prepare a project in MERMAID with sites, management regimes, organizations, and users added, and data sharing policies set up.

• Export your photo benthic quadrat data from CoralNet, including the auxiliary fields. You will need to set up your auxiliary fields to contain Sites and Management Regimes that correspond to what you have added on MERMAID, as well as Transect numbers. You are also free to rename your auxiliary fields. To download your data with its auxiliary fields, navigate to “Images” in a CoralNet project. Under the “Image Actions”, select “Export Annotations, CSV”, and select the optional columns “Image metadata - date and auxiliary fields”, as shown below:

• Open Easy PQT and follow the instructions. Once you open the Easy PQT, it will automatically ask you to authenticate yourself. This way, Easy PQT can provide a list of your projects. Only project(s) that are not a test project will be shown on the list.

• Select the project to which you want to upload your data and upload your CSV data. You can click the “browse” button to find the data you want to upload or drag and drop directly to the upload field.

• Match your CoralNet auxiliary fields with the MERMAID Site, Management, and Transect number you’ve prepared on the app. Once you’re done matching those three columns, Easy PQT will automatically validate them to see if they match the options in the MERMAID project you’ve prepared. If it does not match, you will receive information on which fields do not match and what the available options are. A button to Restart Easy PQT will also appear for you to click and restart the process after fixing the issue(s).

• When all your data in the auxiliary fields are validated, Easy PQT will map your CoralNet labels to MERMAID attributes. If it’s not available in Easy PQT, then the MERMAID Benthic attribute field will be left blank and colored in red. You need to select the right benthic attributes by clicking on the field directly and start typing or clicking on the arrow on the right to show the dropdown options. Once you’re done filling in the blank fields, click on the “Confirm” button to continue. Easy PQT will reshape your data to match the MERMAID template.

• Review your reshaped data, then click the “Continue with ingestion” button to upload your data to MERMAID. If you think the data is incorrect, you can click the “Restart Easy PQT” button to start the process from the beginning or click the “Get help” button to contact us for further assistance. In this section, you can also download the reshaped data in a csv format.

• Upload your reshaped data to MERMAID by clicking the “Continue with ingestion” button on the Easy PQT app. Your uploaded data will appear on your Collecting Page.

• Head to your Collecting Page in the MERMAID app to fill in the rest of the mandatory fields. After uploading your data, there are still some mandatory fields that you need to fill in. Those mandatory fields include depth, transect length surveyed, and quadrat size. East PQT will automatically assign you (a user that uploads the data) as the observer. Change the observer to the right data collector if you are not the one who collects the data. Once you’re done filling those information, you can validate and submit your transects.

Unsubmitted uploaded transects will appear on the Collecting Page of the users who uploaded the data using Easy PQT. You can transfer these unsubmitted sample units to another user through the project’s User Page. Only an admin of a project can perform this action.